[GRASSLIST:7650] R Stats and GRASS primer (wanted)

GRASS GRASS user
1

Even before I can finish my current project I'm looking to the future.

I would like to gather some resources on combining R stats and GRASS. I found tutorial from a while ago at
http://reclus.nhh.no/gc00/gc009.htm
not sure if all the commands are still relavent or if the datasets they use still exist. as its older version of GRASS and R

I wouldn't mind if people submitted more samples of how they used R Stats and GRASS. If they are examples on spearfish data that is even better because we all have it.

Cheers

--
+---------------------------------------------------------------+
|Dave Sampson: Geographic Information System (GIS) Technician |
| |
|Centre for Sustainable Watersheds |
|Cooperative Approaches to Protect Canada's Water Resources |
| |
|14 Water St, P.O Box 280. Portland Ontario, Canada. K0G 1V0 |
|Lat: 44.700 Long: -76.19 |
|www.watersheds.ca gis@watersheds.ca |
+---------------------------------------------------------------+

2

On Wed, 20 Jul 2005, Dave Sampson wrote:

Even before I can finish my current project I'm looking to the future.

Way to go! :slight_smile: I'd like to echo this request, as I'd like to upskill in
this area as well.

I'm providing GIS support to teams with several statisticians/modellers
who are R users. I'm not making much use of GRASS coz I haven't really
needed to, but (looking to the future :slight_smile: I'd like to be able to build up
expertise in GRASS (in addition to what I do now with PostGIS/QGIS/GMT)
with demonstrable links to R.

Personally I believe a well set up PostGIS/GRASS/R suite is
potentially about the most powerful analytical GIS around, and that
working towards such a system is therefore a very useful sxercise.
Throw mapserver/uDIG & others at this and you can even web enable it
without a huge effort. Throw QGIS & you have user friendly browsing &
a nice GRASS GUI.

While I have no immediate use, (but do have an immediate lack of skills
& time) I'd love to see a wiki or some easily accessible resource
providing information a sort of GRASS & R howto, so I could at least keep
in touch with this particular area....

I would like to gather some resources on combining R stats and GRASS. I
found tutorial from a while ago at
http://reclus.nhh.no/gc00/gc009.htm
not sure if all the commands are still relavent or if the datasets they
use still exist. as its older version of GRASS and R

I wouldn't mind if people submitted more samples of how they used R
Stats and GRASS. If they are examples on spearfish data that is even
better because we all have it.

Thanks Dave,

  Brent Wood

3

Hi Dave,

On Wed, Jul 20, 2005 at 05:54:28PM -0400, Dave Sampson wrote:

Even before I can finish my current project I'm looking to the future.

I would like to gather some resources on combining R stats and GRASS. I
found tutorial from a while ago at
http://reclus.nhh.no/gc00/gc009.htm
not sure if all the commands are still relavent or if the datasets they
use still exist. as its older version of GRASS and R

I wouldn't mind if people submitted more samples of how they used R
Stats and GRASS. If they are examples on spearfish data that is even
better because we all have it.

Here we go with some suggestions:

- related web page:
  http://grass.itc.it/statsgrass/index.php
  -> GRASS 6.x: GRASS6-R interface (installation: see here)
  -> Short draft introduction to R/GRASS interface (evolving,
     needs some GRASS 6 updates)
  -> Bivand, R.S., 2005. Interfacing GRASS 6 and R. Status and development directions.
     GRASS Newsletter, Vol.3, pp 11-16, June 2005 (PDF).

- Short Courses:
  http://mpa.itc.it/grasstutor/shortcourse_menu.phtml
  -> Open Source GIS Short Course (2003) - GRASS 5, but maybe still
     interesting anyway
  -> Open Source Geoinformatics with GRASS GIS (2005) - GRASS 6
     (I guess you know this one :slight_smile:

- R spatial projects
  http://agec221.agecon.uiuc.edu/csiss/Rgeo/

More forthcoming...

Markus

--
Markus Neteler <neteler itc it> http://mpa.itc.it
ITC-irst - Centro per la Ricerca Scientifica e Tecnologica
MPBA - Predictive Models for Biol. & Environ. Data Analysis
Via Sommarive, 18 - 38050 Povo (Trento), Italy

4

Hi, List,

I also want to make R/GRASS6.0 work on my machine. Is there a special
installation when GRASS sitting on the server and I run R/GRASS on my local
Suse OS system?

Feng

On Thursday 21 July 2005 03:15, Markus Neteler wrote:

Hi Dave,

On Wed, Jul 20, 2005 at 05:54:28PM -0400, Dave Sampson wrote:
> Even before I can finish my current project I'm looking to the future.
>
> I would like to gather some resources on combining R stats and GRASS. I
> found tutorial from a while ago at
> http://reclus.nhh.no/gc00/gc009.htm
> not sure if all the commands are still relavent or if the datasets they
> use still exist. as its older version of GRASS and R
>
> I wouldn't mind if people submitted more samples of how they used R
> Stats and GRASS. If they are examples on spearfish data that is even
> better because we all have it.

Here we go with some suggestions:

- related web page:
  http://grass.itc.it/statsgrass/index.php
  -> GRASS 6.x: GRASS6-R interface (installation: see here)
  -> Short draft introduction to R/GRASS interface (evolving,
     needs some GRASS 6 updates)
  -> Bivand, R.S., 2005. Interfacing GRASS 6 and R. Status and development
directions. GRASS Newsletter, Vol.3, pp 11-16, June 2005 (PDF).

- Short Courses:
  http://mpa.itc.it/grasstutor/shortcourse_menu.phtml
  -> Open Source GIS Short Course (2003) - GRASS 5, but maybe still
     interesting anyway
  -> Open Source Geoinformatics with GRASS GIS (2005) - GRASS 6
     (I guess you know this one :slight_smile:

- R spatial projects
  http://agec221.agecon.uiuc.edu/csiss/Rgeo/

More forthcoming...

Markus

5

hi, Markus,

When I installing the R/GRASS6.0 interface using your instruction , the
following error showed:

install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)

--- Please select a CRAN mirror for use in this session ---
Error in inherits(x, "factor") : Object "res" not found

what happened?

Thanks,

Feng

On Thursday 21 July 2005 03:15, Markus Neteler wrote:

[GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)

From:
Markus Neteler

6

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:

hi, Markus,

When I installing the R/GRASS6.0 interface using your instruction , the
following error showed:

> install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
--- Please select a CRAN mirror for use in this session ---
Error in inherits(x, "factor") : Object "res" not found

what happened?

Thanks,

Feng

On Thursday 21 July 2005 03:15, Markus Neteler wrote:
> [GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)
>
> From:
> Markus Neteler

--
Markus Neteler <neteler itc it> http://mpa.itc.it
ITC-irst - Centro per la Ricerca Scientifica e Tecnologica
MPBA - Predictive Models for Biol. & Environ. Data Analysis
Via Sommarive, 18 - 38050 Povo (Trento), Italy

7

This does not happen is a graphic window is not active (e.g. for installations
over ssh, or if root does not have a graphical window).
The solution is to specify the mirror to use.
All the best.
pc
At 10:04, sabato 23 luglio 2005, Markus Neteler has probably written:

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
> hi, Markus,
>
> When I installing the R/GRASS6.0 interface using your instruction , the
>
> following error showed:
> > install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
>
> --- Please select a CRAN mirror for use in this session ---
> Error in inherits(x, "factor") : Object "res" not found
>
> what happened?
>
> Thanks,
>
> Feng
>
> On Thursday 21 July 2005 03:15, Markus Neteler wrote:
> > [GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)
> >
> > From:
> > Markus Neteler

--
Paolo Cavallini
cavallini@faunalia.it www.faunalia.it www.faunalia.com
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy Tel: (+39)348-3801953

8

Hi, Makkus,

If I use my own user's root directory, the mirror site menu will show up, but
the following errors show up:

mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying

The downloaded packages are in
        /tmp/Rtmpny7325/downloaded_packages
Warning messages:
1: installation of package 'abind' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
2: installation of package 'pixmap' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
3: installation of package 'RColorBrewer' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
4: installation of package 'splancs' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
5: installation of package 'sp' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
6: installation of package 'maptools' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)
7: installation of package 'rgdal' had non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"), dependencies = TRUE)

Thanks,

Feng

On Saturday 23 July 2005 02:04, Markus Neteler wrote:

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
> hi, Markus,
>
> When I installing the R/GRASS6.0 interface using your instruction , the
>
> following error showed:
> > install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
>
> --- Please select a CRAN mirror for use in this session ---
> Error in inherits(x, "factor") : Object "res" not found
>
> what happened?
>
> Thanks,
>
> Feng
>
> On Thursday 21 July 2005 03:15, Markus Neteler wrote:
> > [GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)
> >
> > From:
> > Markus Neteler

9

Hi Feng

It seems that you are not doing it as super user.
Change to SU mode; then start R and install.packages

HTH

Jaime

--- Feng Tan <feng@lynxseismicdata.com> escribió:

Hi, Makkus,

If I use my own user's root directory, the mirror
site menu will show up, but
the following errors show up:

mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying
mkdir: cannot create directory
`/usr/lib/R/library/00LOCK': Permission denied
ERROR: failed to lock directory '/usr/lib/R/library'
for modifying

The downloaded packages are in
        /tmp/Rtmpny7325/downloaded_packages
Warning messages:
1: installation of package 'abind' had non-zero exit
status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
2: installation of package 'pixmap' had non-zero
exit status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
3: installation of package 'RColorBrewer' had
non-zero exit status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
4: installation of package 'splancs' had non-zero
exit status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
5: installation of package 'sp' had non-zero exit
status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
6: installation of package 'maptools' had non-zero
exit status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)
7: installation of package 'rgdal' had non-zero exit
status in:
install.packages(c("sp", "rgdal", "maptools"),
dependencies = TRUE)

Thanks,

Feng

On Saturday 23 July 2005 02:04, Markus Neteler
wrote:
> Hi Feng,
>
> I always launched update.packages() before
installing the
> sp things. Then a Tcl window pops up where I
select a mirror
> site.
>
> Or: probably you tcl/tk libraries are not
installed [properly]?
>
> Markus
>
> On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan
wrote:
> > hi, Markus,
> >
> > When I installing the R/GRASS6.0 interface using
your instruction , the
> >
> > following error showed:
> > > install.packages(c("sp","rgdal","maptools"),
dependencies=TRUE)
> >
> > --- Please select a CRAN mirror for use in this
session ---
> > Error in inherits(x, "factor") : Object "res"
not found
> >
> > what happened?
> >
> > Thanks,
> >
> > Feng
> >
> > On Thursday 21 July 2005 03:15, Markus Neteler
wrote:
> > > [GRASSLIST:7657] Re: R Stats and GRASS primer
(wanted)
> > >
> > > From:
> > > Markus Neteler

__________________________________________________
Correo Yahoo!
Espacio para todos tus mensajes, antivirus y antispam ¡gratis!
Regístrate ya - http://correo.espanol.yahoo.com/

10

Hi, List,

Thanks for your help!! I have successfully installed GRASS6.0/R. It works on
spearfish test dataset. But when I run my own dataset which have worked for
GRASS5.7/R does not work for GRASS6.0/R, it said:"cannot find function
rast.get() ". Please help!!

Thanks!

Feng

On Saturday 23 July 2005 02:04, Markus Neteler wrote:

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
> hi, Markus,
>
> When I installing the R/GRASS6.0 interface using your instruction , the
>
> following error showed:
> > install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
>
> --- Please select a CRAN mirror for use in this session ---
> Error in inherits(x, "factor") : Object "res" not found
>
> what happened?
>
> Thanks,
>
> Feng
>
> On Thursday 21 July 2005 03:15, Markus Neteler wrote:
> > [GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)
> >
> > From:
> > Markus Neteler

11

Feng,

Go to CRAN (http://cran.r-project.org/) to the Newsletter section and get the Volume 5/1, May 2005 issue. There is an article on the new GRASS/R interface that's needed with R 2.1 & GRASS 6.x. Hope this helps.

Tom

Feng Tan wrote:

Hi, List,

Thanks for your help!! I have successfully installed GRASS6.0/R. It works on spearfish test dataset. But when I run my own dataset which have worked for GRASS5.7/R does not work for GRASS6.0/R, it said:"cannot find function rast.get() ". Please help!!

Thanks!

Feng

On Saturday 23 July 2005 02:04, Markus Neteler wrote:

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
   

hi, Markus,

When I installing the R/GRASS6.0 interface using your instruction , the

following error showed:
     

install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
       

--- Please select a CRAN mirror for use in this session ---
Error in inherits(x, "factor") : Object "res" not found

what happened?

Thanks,

Feng

On Thursday 21 July 2005 03:15, Markus Neteler wrote:
     

[GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)

From:
Markus Neteler
       
--
Thomas E Adams
National Weather Service
Ohio River Forecast Center
1901 South State Route 134
Wilmington, OH 45177

EMAIL: thomas.adams@noaa.gov

VOICE: 937-383-0528
FAX: 937-383-0033

12

On Tue, 16 Aug 2005, Thomas Adams wrote:

Feng,

Go to CRAN (http://cran.r-project.org/) to the Newsletter section and
get the Volume 5/1, May 2005 issue. There is an article on the new
GRASS/R interface that's needed with R 2.1 & GRASS 6.x. Hope this helps.

Please make that: http://grass.itc.it/newsletter/index.php - the article
is the the GRASS Newsletter volume 3, June 2005, pp. 11-16, and an erratum
is there too for difficulties installing on a server rather than a
workstation.

rast.get() is replaced in the new framework by readFLOATsp() and
readCELLsp(), so you will have to change your code; in addition, the
objects returned are different too.

Roger

Tom

Feng Tan wrote:

>Hi, List,
>
>Thanks for your help. I have successfully installed GRASS6.0/R. It works on
>spearfish test dataset. But when I run my own dataset which have worked for
>GRASS5.7/R does not work for GRASS6.0/R, it said:"cannot find function
>rast.get() ". Please help!!
>
>Thanks!
>
>Feng
>
>
>
>On Saturday 23 July 2005 02:04, Markus Neteler wrote:
>
>
>>Hi Feng,
>>
>>I always launched update.packages() before installing the
>>sp things. Then a Tcl window pops up where I select a mirror
>>site.
>>
>>Or: probably you tcl/tk libraries are not installed [properly]?
>>
>>Markus
>>
>>On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
>>
>>
>>>hi, Markus,
>>>
>>>When I installing the R/GRASS6.0 interface using your instruction , the
>>>
>>>following error showed:
>>>
>>>
>>>>install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
>>>>
>>>>
>>>--- Please select a CRAN mirror for use in this session ---
>>>Error in inherits(x, "factor") : Object "res" not found
>>>
>>>what happened?
>>>
>>>Thanks,
>>>
>>>Feng
>>>
>>>On Thursday 21 July 2005 03:15, Markus Neteler wrote:
>>>
>>>
>>>>[GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)
>>>>
>>>>From:
>>>>Markus Neteler
>>>>
>>>>
>
>
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand@nhh.no

13

Roger & Feng,

Ooops. Should have double checked before I posted. Thanks for the correction, Roger! BTW, I should have my plans to pass through Bergen in Oct. on my way to Tromso settled by the end of August. I'll let you know.

Regards,
Tom

Roger Bivand wrote:

On Tue, 16 Aug 2005, Thomas Adams wrote:

Feng,

Go to CRAN (http://cran.r-project.org/) to the Newsletter section and get the Volume 5/1, May 2005 issue. There is an article on the new GRASS/R interface that's needed with R 2.1 & GRASS 6.x. Hope this helps.
   
Please make that: http://grass.itc.it/newsletter/index.php - the article is the the GRASS Newsletter volume 3, June 2005, pp. 11-16, and an erratum is there too for difficulties installing on a server rather than a workstation.

rast.get() is replaced in the new framework by readFLOATsp() and readCELLsp(), so you will have to change your code; in addition, the objects returned are different too.

Roger

Tom

Feng Tan wrote:

Hi, List,

Thanks for your help. I have successfully installed GRASS6.0/R. It works on spearfish test dataset. But when I run my own dataset which have worked for GRASS5.7/R does not work for GRASS6.0/R, it said:"cannot find function rast.get() ". Please help!!

Thanks!

Feng

On Saturday 23 July 2005 02:04, Markus Neteler wrote:

Hi Feng,

I always launched update.packages() before installing the
sp things. Then a Tcl window pops up where I select a mirror
site.

Or: probably you tcl/tk libraries are not installed [properly]?

Markus

On Fri, Jul 22, 2005 at 09:23:44AM -0600, Feng Tan wrote:
  

hi, Markus,

When I installing the R/GRASS6.0 interface using your instruction , the

following error showed:
    

install.packages(c("sp","rgdal","maptools"), dependencies=TRUE)
      

--- Please select a CRAN mirror for use in this session ---
Error in inherits(x, "factor") : Object "res" not found

what happened?

Thanks,

Feng

On Thursday 21 July 2005 03:15, Markus Neteler wrote:
    

[GRASSLIST:7657] Re: R Stats and GRASS primer (wanted)

From:
Markus Neteler
      
--
Thomas E Adams
National Weather Service
Ohio River Forecast Center
1901 South State Route 134
Wilmington, OH 45177

EMAIL: thomas.adams@noaa.gov

VOICE: 937-383-0528
FAX: 937-383-0033